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Introduction
This document is a section of the Administration Guide.
LexEVS Configuration Options
The LexEVS software, documentation, indexes, and system logs are located in the {LEXBIG_DIRECTORY} (e.g.,
...
/usr/local/packages/LexBIG
...
or
...
c:\lexbig).
...
These
...
files
...
may
...
be
...
part
...
of
...
the
...
local
...
file
...
system
...
and
...
may
...
require
...
backup
...
procedures
...
to
...
meet
...
servicability
...
and
...
recovery
...
requirements
...
for
...
your
...
organization.
...
LexEVS
...
uses
...
basic
...
database
...
indexes,
...
but
...
also
...
includes
...
a
...
separate
...
indexing
...
facility
...
using
...
Apache
...
Lucene.
...
Lucene
...
Index
...
files
...
are
...
stored
...
in
...
a
...
directory
...
as
...
specified
...
in
...
the
...
lbconfig.props
...
file
...
index_location
...
variable.
...
What
...
Is
...
a
...
Coding
...
Scheme
...
Manifest?
...
A
...
"Coding
...
Scheme
...
Manifest"
...
(or
...
simply
...
"manifest"
...
as
...
used
...
interchangeably
...
in
...
this
...
document)
...
allows
...
the
...
user
...
to
...
set
...
values
...
for
...
a
...
coding
...
scheme
...
while
...
loading
...
or
...
converting
...
a
...
LexGrid
...
"XML",
...
"NCI
...
MetaThesaurus",
...
"NCI
...
OWL","OWL",
...
"OBO",
...
"UMLS
...
RRF
...
File",
...
or"HL7
...
RIM
...
Database"
...
source
...
to
...
LexGrid
...
format.
...
What Is a Coding Scheme?
Coding Scheme is the term that is used to represent an ontology/terminology being loaded or converted. In the LexGrid data model a terminology is represented as a coding scheme and it can reference other coding schemes. An example of coding scheme is "Amino Acid" which is described in the "amino acid.owl" file.
A Coding Scheme has some meta information about it; values like 'formal name', 'local names', 'default language', 'version', 'copyright', 'sources' to name some.
Why Do We Need a Coding Scheme Manifest?
When a terminology is being converted to the LexGrid data model from its native format (in this case OWL), Coding Scheme information is read from the source file. Sometimes values may be missing (not provided or invalid) or the author/user of the terminology wants to override or set default values despite (or in addition to) what is provided in the source file. This can be accomplished using "manifest" files along with the source file.
How Do We Create a Coding Scheme Manifest File?
A coding scheme manifest file is a valid XML file, conforming to the schema defined by: http://LexGrid.org/schema/LexBIG/2007/01/CodingSchemeManifestList.xsd
...
This
...
XML
...
file
...
can
...
define
...
values
...
for
...
one
...
or
...
more
...
coding
...
schemes
...
you
...
are
...
dealing
...
with.
...
Some
...
coding
...
scheme
...
meta-information
...
may
...
not
...
easily
...
map
...
to
...
information
...
in
...
the
...
source
...
file.
...
In
...
this
...
case
...
a
...
manifest
...
file
...
is
...
of
...
great
...
help
...
to
...
bridge
...
the
...
gap
...
and
...
control
...
the
...
information
...
flow
...
while
...
mapping
...
to
...
the
...
LexGrid
...
model.
...
A
...
detailed
...
model
...
of
...
the
...
LexGrid
...
Coding
...
Scheme
...
and
...
its
...
fields
...
can
...
be
...
found
...
online.
...
Structure
...
of
...
the
...
schema
...
for
...
the
...
manifest
...
file
...
is
...
explained
...
in
...
the
...
following
...
table
...
(manifest
...
components
...
refer
...
to
...
the
...
original
...
LexGrid
...
model
...
schema
...
namespaces
...
and
...
types):
...
- Coding
...
- Scheme
...
- Manifest
...
- entry
...
- field:
...
- id
- Type:
...
- lgCommon:registeredName
...
- Required:
...
- Yes
...
- Override
...
- flag
...
- set:
...
- Not
...
- applicable
...
- Description:
...
The
...
- registered
...
- name
...
- is
...
- the
...
- key
...
- used
...
- to
...
- find
...
- a
...
- coding
...
- scheme
...
- (for
...
- example
...
- a
...
- unique
...
- URL
...
- or
...
- namespace
...
- by
...
- which
...
- other
...
- people
...
- access
...
- same
...
- coding
...
- scheme).
...
- This
...
- String
...
- value
...
- will
...
- be
...
- used
...
- to
...
- identify
...
- the
...
- manifest
...
- entry
...
- in
...
- the
...
- manifest
...
- file
...
- for
...
- the
...
- coding
...
- scheme
...
- too.
...
- For
...
- example
...
- the
...
- registered
...
- name
...
- for
...
- coding
...
- scheme
...
- "Amino-acid"
...
- is
...
...
- This
...
- string
...
- is
...
- also
...
- set
...
- as
...
- the
...
- coding
...
- scheme's
...
- registered
...
- name
...
- field
...
- in
...
- the
...
- LexGrid
...
- model.
...
- Coding
...
- Scheme
...
- Manifest
...
- entry
...
- field:
...
- codingScheme
- Type:
...
- lgBuiltin:localId
...
- Required:
...
- No
...
- Override
...
- flag
...
- set:
...
- Yes
...
- Description:
...
This
...
- value
...
- will
...
- be
...
- set
...
- for
...
- 'coding
...
- scheme
...
- name'
...
- in
...
- the
...
- LexGrid
...
- format
...
- counterpart.
...
- If
...
- the
...
- override
...
- flag
...
- is
...
- set
...
- to
...
- 'true',
...
- the
...
- value
...
- provided
...
- in
...
- the
...
- source
...
- file
...
- will
...
- be
...
- replaced
...
- with
...
- this
...
- one.
...
- Otherwise,
...
- this
...
- value
...
- is
...
- treated
...
- as
...
- a
...
- default
...
- value
...
- and
...
- used
...
- only
...
- if
...
- the
...
- value
...
- is
...
- not
...
- provided
...
- in
...
- the
...
- source
...
- file.
...
- Coding
...
- Scheme
...
- Manifest
...
- entry
...
- field:
...
- entityDescription
- Type:
...
- lgCommon:entityDescription
...
- Required:
...
- No
...
- Override
...
- flag
...
- set:
...
- Yes
...
- Description:
...
This
...
- value
...
- will
...
- be
...
- set
...
- for
...
- 'coding
...
- scheme
...
- description'
...
- in
...
- the
...
- LexGrid
...
- format
...
- counterpart.
...
- If
...
- the
...
- override
...
- flag
...
- is
...
- set
...
- to
...
- 'true',
...
- the
...
- value
...
- provided
...
- in
...
- the
...
- source
...
- file
...
- will
...
- be
...
- replaced
...
- with
...
- this
...
- one.
...
- Otherwise,
...
- this
...
- value
...
- is
...
- treated
...
- as
...
- a
...
- default
...
- value
...
- and
...
- used
...
- only
...
- if
...
- the
...
- value
...
- is
...
- not
...
- provided
...
- in
...
- the
...
- source
...
- file.
...
- Coding
...
- Scheme
...
- Manifest
...
- entry
...
- field:
...
- formalName
- Type:
...
- lgBuiltin:tsCaseIgnoreIA5String
...
- Required:
...
- No
...
- Override
...
- flag
...
- set:
...
- Yes
...
- Description:
...
This
...
- value
...
- will
...
- be
...
- set
...
- for
...
- 'coding
...
- scheme
...
- formal
...
- name'
...
- in
...
- the
...
- LexGrid
...
- format
...
- counterpart.
...
- If
...
- the
...
- override
...
- flag
...
- is
...
- set
...
- to
...
- 'true',
...
- the
...
- value
...
- provided
...
- in
...
- the
...
- source
...
- file
...
- will
...
- be
...
- replaced
...
- with
...
- this
...
- one.
...
- Otherwise,
...
- this
...
- value
...
- is
...
- treated
...
- as
...
- a
...
- default
...
- value
...
- and
...
- used
...
- only
...
- if
...
- the
...
- value
...
- is
...
- not
...
- provided
...
- in
...
- the
...
- source
...
- file.
...
- Coding
...
- Scheme
...
- Manifest
...
- entry
...
- field:
...
- registeredName
- Type:
...
- lgCommon:registeredName
...
- Required:
...
- No
...
- Override
...
- flag
...
- set:
...
- Yes
...
- Description:
...
This
...
- value
...
- will
...
- be
...
- set
...
- for
...
- 'coding
...
- scheme
...
- registered
...
- name'
...
- in
...
- the
...
- LexGrid
...
- format
...
- counterpart.
...
- If
...
- the
...
- override
...
- flag
...
- is
...
- set
...
- to
...
- 'true',
...
- the
...
- value
...
- provided
...
- in
...
- the
...
- source
...
- file
...
- will
...
- be
...
- replaced
...
- with
...
- this
...
- one.
...
- Otherwise,
...
- this
...
- value
...
- is
...
- treated
...
- as
...
- a
...
- default
...
- value
...
- and
...
- used
...
- only
...
- if
...
- the
...
- value
...
- is
...
- not
...
- provided
...
- in
...
- the
...
- source
...
- file.
...
- Coding
...
- Scheme
...
- Manifest
...
- entry
...
- field:
...
- defaultLanguage
- Type:
...
- lgCommon:defaultLanguage
...
- Required:
...
- No
...
- Override
...
- flag
...
- set:
...
- Yes
...
- Description:
...
This
...
- value
...
- will
...
- be
...
- set
...
- for
...
- 'coding
...
- scheme
...
- default
...
- language'
...
- in
...
- the
...
- LexGrid
...
- format
...
- counterpart.
...
- If
...
- the
...
- override
...
- flag
...
- is
...
- set
...
- to
...
- 'true',
...
- the
...
- value
...
- provided
...
- in
...
- the
...
- source
...
- file
...
- will
...
- be
...
- replaced
...
- with
...
- this
...
- one.
...
- Otherwise,
...
- this
...
- value
...
- is
...
- treated
...
- as
...
- a
...
- default
...
- value
...
- and
...
- used
...
- only
...
- if
...
- the
...
- value
...
- is
...
- not
...
- provided
...
- in
...
- the
...
- source
...
- file.
...
- Coding
...
- Scheme
...
- Manifest
...
- entry
...
- field:
...
- representsVersion
- Type:
...
- lgCommon:version
...
- Required:
...
- No
...
- Override
...
- flag
...
- set:
...
- Yes
...
- Description:
...
This
...
- value
...
- will
...
- be
...
- set
...
- for
...
- 'coding
...
- scheme
...
- version'
...
- in
...
- the
...
- LexGrid
...
- format
...
- counterpart.
...
- If
...
- the
...
- override
...
- flag
...
- is
...
set
...
- to
...
- 'true',
...
- the
...
- value
...
- provided
...
- in
...
- the
...
- source
...
- file
...
- will
...
- be
...
- replaced
...
- with
...
- this
...
- one.
...
- Otherwise,
...
- this
...
- value
...
- is
...
treated
...
- as
...
- a
...
- default
...
- value
...
- and
...
- used
...
- only
...
- if
...
- the
...
- value
...
- is
...
- not
...
- provided
...
- in
...
- the
...
- source
...
- file.
...
- Coding
...
- Scheme
...
- Manifest
...
- entry
...
- field:
...
- localName
- Type:
...
- lgBuiltin:tsCaseIgnoreIA5String
...
- Required:
...
- No
...
- "To
...
- Add"
...
- flag
...
- set:
...
- Yes
...
- Description:
...
This
...
- value
...
- will
...
- be
...
- added
...
- for
...
- 'coding
...
- scheme
...
- local
...
- names'.
...
- If
...
- the
...
- add
...
- flag
...
- is
...
- set
...
- to
...
- 'true',
...
- this
...
- value
...
- will
...
be
...
- added
...
- to
...
- the
...
- list
...
- of
...
- local
...
- names
...
- (if
...
- not
...
- there
...
- already).
...
- Otherwise,
...
- this
...
- value
...
- is
...
- treated
...
- as
...
- the
...
- default
...
value
...
- and
...
- used
...
- only
...
- if
...
- the
...
- value
...
- is
...
- not
...
- provided
...
- in
...
- the
...
- source
...
- file.
...
- Coding
...
- Scheme
...
- Manifest
...
- entry
...
- field:
...
- source
- Type:
...
- lgCommon:source
...
- Required:
...
- No
...
- "To
...
- Add"
...
- flag
...
- set:
...
- Yes
...
- Description:
...
This
...
- value
...
- will
...
- be
...
- added
...
- for
...
- 'coding
...
- scheme
...
- sources'.
...
- If
...
- the
...
- add
...
- flag
...
- is
...
- set
...
- to
...
- 'true',
...
- this
...
- value
...
- will
...
- be
...
added
...
- to
...
- the
...
- list
...
- of
...
- sources
...
- (if
...
- not
...
- there
...
- already).
...
- Otherwise,
...
- this
...
- value
...
- is
...
- treated
...
- as
...
- the
...
- default
...
- value
...
and
...
- used
...
- only
...
- if
...
- the
...
- value
...
- is
...
- not
...
- provided
...
- in
...
- the
...
- source
...
- file.
...
- Coding
...
- Scheme
...
- Manifest
...
- entry
...
- field:
...
- copyright
- Type:
...
- lgCommon:text
...
- Required:
...
- No
...
- Override
...
- flag
...
- set:
...
- Yes
...
- Description:
...
This
...
- value
...
- will
...
- be
...
- set
...
- for
...
- 'coding
...
- scheme
...
- copyright'
...
- in
...
- the
...
- LexGrid
...
- format
...
- counterpart.
...
- If
...
- the
...
- override
...
- flag
...
is
...
- set
...
- to
...
- 'true',
...
- the
...
- value
...
- provided
...
- in
...
- the
...
- source
...
- file
...
- will
...
- be
...
- replaced
...
- with
...
- this
...
- one.
...
- Otherwise,
...
- this
...
- value
...
is
...
- treated
...
- as
...
- a
...
- default
...
- value
...
- and
...
- used
...
- only
...
- if
...
- the
...
- value
...
- is
...
- not
...
- provided
...
- in
...
- the
...
- source
...
- file.
...
- Coding
...
- Scheme
...
- Manifest
...
- entry
...
- field:
...
- mappings
- Type:
...
- lgCS:mappings
...
- Required:
...
- No
...
- "To
...
- Add"
...
- flag
...
- set:
...
- Yes
...
- Description:
...
This
...
- value
...
- will
...
- be
...
- added
...
- for
...
- 'coding
...
- scheme
...
- mappings'.
...
- If
...
- the
...
- add
...
- flag
...
- is
...
- set
...
- to
...
- 'true',
...
- this
...
- value
...
- will
...
- be
...
added
...
- to
...
- the
...
- list
...
- of
...
- mappings
...
- (if
...
- not
...
- there
...
- already).
...
- Otherwise,
...
- this
...
- value
...
- is
...
- treated
...
- as
...
- the
...
- default
...
- value
...
and
...
- used
...
- only
...
- if
...
- the
...
- value
...
- is
...
- not
...
- provided
...
- in
...
- the
...
- source
...
- file.
...
- Coding
...
- Scheme
...
- Manifest
...
- entry
...
- field:
...
- associationDefinitions
- Type:
...
- lgRel:association
...
- Required:
...
- No
...
- "To
...
- Add"
...
- flag
...
- set:
...
- Yes
...
- Description:
...
This
...
- value
...
- will
...
- be
...
- added
...
- for
...
- 'coding
...
- scheme
...
- associations'.
...
- If
...
- the
...
- add
...
- flag
...
- is
...
- set
...
- to
...
- 'true',
...
- this
...
- value
...
- will
...
be
...
- added
...
- to
...
- the
...
- list
...
- of
...
- associations
...
- (if
...
- not
...
- there
...
- already).
...
- Otherwise,
...
- this
...
- value
...
- is
...
- treated
...
- as
...
- the
...
- default
...
value
...
- and
...
- used
...
- only
...
- if
...
- the
...
- value
...
- is
...
- not
...
- provided
...
- in
...
- the
...
- source
...
- file.
...
| Info | ||
|---|---|---|
| ||
This option is used internally by the system to provide default recognition of some common associations. It is typically not necessary to provide this value, however, since association definitions are automatically derived from the source. |
What Code Changes May Be Required To Use a Manifest File?
If you want to use the manifest file, you can supply the manifest file URI to the following methods when Loading NCI OWL or generic OWL Loads:
"org.LexGrid.LexBIG.Extensions.Load.OWL_Loader.load()"
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"org.LexGrid.LexBIG.Extensions.Load.OWL_Loader.validate()"
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For all other manifest loads the following methods are employed.
{include:SupplyNonOwlFileUri
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Configuration
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| } This section provides an overview of the components as related to system adminstration, backup, and recovery. Individual organizations may have their own backup and diaster recovery procedure. In every case users created for use by the LexEVS application must have read, write and delete access to the dbms instance. {warning} Database systems as described in the section _Required Software—Not Included in LexEVS_ provide the storage for vocabularies loaded into LexEVS. For each vocabulary version loaded into LexEVS a new database is created. As defined in the {{lbconfig.props}} files the {{db_prefix}} variable is used to create the database name. For example with {{db_prefix=lexbig}}, each new vocabulary version that is loaded a new database is created using an incremental counter. * lexbig1 * lexbig2 * lexbig3 * lexbigN Depending on backup strategy, system administrators will need to be aware that multiple databases are being created and may need backup procedures to meet servicability and recovery requirements for your organization. h2. MySQL Configuration [MySQL properties|3 - Installing LexEVS 5.x Local Runtime#MySQL Properties] h2. PostGreSQL Configuration [PostgreSQL properties|3 - Installing LexEVS 5.x Local Runtime#PostgreSQL Properties] {scrollbar:icons=false} |
Database systems as described in the section Required Software—Not Included in LexEVS provide the storage for vocabularies loaded into LexEVS. For each vocabulary version loaded into LexEVS a new database is created. As defined in the lbconfig.props files the db_prefix variable is used to create the database name.
For example with db_prefix=lexbig, each new vocabulary version that is loaded a new database is created using an incremental counter.
- lexbig1
- lexbig2
- lexbig3
- lexbigN
Depending on backup strategy, system administrators will need to be aware that multiple databases are being created and may need backup procedures to meet servicability and recovery requirements for your organization.
MySQL Configuration
PostGreSQL Configuration
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